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Notes on Heather's notes

https://github.com/r-devel/rcwg/blob/main/working_documents/install_r_macos.md

I worked through Heather's notes during the RProject Sprint, on Sept 1st 2023, with assistance from George Stagg.

Issues

  1. In Install Prerequisites section, point 7, it appears we do still need to install subversion, but install.libs("subversion", dep = FALSE) didn't work for me (at least then running which svn in the terminal didn't find it). So I installed it via brew instead: brew install svn which appears to have worked fine.

    HT: I also had Subversion installed from Homebrew. I tried uninstalling it (brew uninstall subversion) and installing with install.libs and it worked fine (running which svn returned /opt/R/arm64/bin/svn as expected). So possible a local issue, will add installation via Homebrew as a troubleshooting workaround.

  2. In Build R section, George reckons that the build directory looks strange. He would have

    export TOP_SRCDIR="$HOME/R-devel/svn"
svn checkout https://svn.r-project.org/R/trunk/ "$TOP_SRCDIR"

    and

    export BUILDDIR="$HOME/R-devel/build"
mkdir -p "$BUILDDIR"
cd "$BUILDDIR"

    This way, build directory and source are both within the R-devel folder

    build rather than bin/R since building R will create bin/R

    HT: Agree the current directories are not ideal - they were to match what we currently have in the dev guide for Linux: https://contributor.r-project.org/rdevguide/GetStart.html#linux. But we had a similar discussion when working on the R Dev Container and came up with

    /workspaces/r-dev-env/build

    /workspaces/r-dev-env/svn

    with the idea that if you had multiple builds of R you could have them nested under those directories. Will poll R Contributors to help decide what is best.

    (gone with second option for now)

  3. In Build R, point 3 for Apple Silicon only, in line before EOF, need to add CPPFLAGS to link to the headers for liblzma:

    CPPFLAGS="-isystem $LOCAL/include -I/opt/R/arm64/include"

    (This will take precedence over the CPPFLAGS in previous chunk, which is what we want)

    HT: Fine, added.

  4. Why RSwitch and not rig?

    HT: simplest tool for this purpose - enables switching while people can carry on installing R as they have done before. But not needed if people are already using rig, so have added some comments about this.

  5. Getting stuck with gfortran. It's installed in /opt/gfortran/bin/gfortran and the configure flag is set to FC="/opt/gfortran/bin/gfortran -mtune=native" but make seems to be looking for /opt/R/arm64/gfortran/bin/gfortran

    Issues with gfortran Getting error when running make related to gfortran and nlme:

    /opt/R/arm64/gfortran/bin/gfortran: No such file or directory

    Not sure why nlme is looking for gfortran there, rather than /opt/gfortran/bin/gfortran. Have tried adding this to PATH with export PATH="/opt/gfortran/bin:$PATH" and then removing the FC flag from config.site (it's not needed once gfortran is in the PATH).

    Try a symlink:

    mkdir -p /opt/R/arm64/gfortran/bin
ln -s /opt/gfortran/bin/gfortran /opt/R/arm64/gfortran/bin/gfortran

    This works but it's hacky. To undo this, rm /opt/R/arm64/gfortran/bin/gfortran

    An alternative for gfortran, since the problem is when nlme is to not do step 1 of Build R, i.e. do not download recommended packages, then will also need additional config flag (need to check this)

    --without-recommended-packages

    HT: Fixed by updating LDFLAGS. Not sure if this applies to Intel too.

  6. Need to install java or turn it off!

    "$TOP_SRCDIR/configure" --enable-R-framework --disable-java

    I've gone with turning it off, but would probably be better to install!

    HT: --disable-java just disables the check for Java, we could add this option but it's not essential (keep instructions as simple as possible). I'm not sure if we need Java to work with base R and recommended packages only. If we do, need to add instructions based on https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Java-_0028macOS_0029 (Java cannot be installed with install.lib.) But instructions easier to maintain if we can manage without.

General notes

After make check, if still in build directory, need to run bin/R to start newly build

HT: Fixed by adding make install step.